A diverse uncultivated microbial community is responsible for organic matter degradation in the Black Sea sulphidic zone

Discovering Hidden Archaeal and Bacterial Lipid Producers in a Euxinic Marine System

Bacterial membrane lipids are typically characterised by fatty acid bilayers linked through ester bonds, whereas those of Archaea are characterised by ether-linked isoprenoids forming bilayers or monolayers of membrane-spanning lipids known as isoprenoidal glycerol dialkyl glycerol tetraethers (isoGDGTs). However, this understanding has been reconsidered with the identification of branched GDGTs (brGDGTs), which are membrane-spanning ether-bound branched alkyl fatty acids of bacterial origin, though their producers are often unidentified. The limited availability of microbial cultures constrains the understanding of the biological sources of these membrane lipids, thus limiting their use as biomarkers. To address this issue, we identified membrane lipids in the Black Sea using high-resolution accurate mass/mass spectrometry and inferred their potential producers by targeting lipid biosynthetic pathways encoded on the metagenome, in metagenome-assembled genomes and unbinned scaffolds. We also identified brGDGTs and highly branched GDGTs in the suboxic and euxinic waters, potentially attributed to Planctomycetota, Cloacimonadota, Desulfobacterota, Chloroflexota, Actinobacteria and Myxococcota-based on their lipid biosynthetic genomic potential. These findings introduce new possibilities for using specific brGDGTs as biomarkers of anoxic conditions in marine environments and highlight the role of these membrane lipids in microbial adaptation.

Comparing field and lab quantitative stable isotope probing for nitrogen assimilation in soil microbes

Soil microbial communities play crucial roles in nutrient cycling and can help retain nitrogen in agricultural soils. Quantitative stable isotope probing (qSIP) is a useful method for investigating taxon-specific microbial growth and utilization of specific nutrients, such as nitrogen (N). Typically, qSIP is performed in a highly controlled lab setting, so the field relevance of lab qSIP studies remains unknown. We conducted and compared tandem lab and field qSIP to quantify the assimilation of 15N by maize-associated soil prokaryotic communities at two agricultural sites. Here, we show that field qSIP with 15N can be used to measure taxon-specific microbial N assimilation. Relative 15N assimilation rates were generally lower in the field, and the magnitude of this difference varied by site. Rates differed by method (lab vs field) for 19% of the top N assimilating genera. The field and lab measures were more comparable when relative assimilation rates were weighted by relative abundance to estimate the proportion of N assimilated by each genus with only ~10% of taxa differing by method. Of those that differed, the taxa consistently higher in the lab were inclined to have opportunistic lifestyle strategies, whereas those higher in the field had niches reliant on plant roots or in-tact soil structure (biofilms, mycelia). This study demonstrates that 15N-qSIP can be successfully performed using field-incubated soils to identify microbial allies in N retention and highlights the strengths and limitations of field and lab qSIP approaches.

IMPORTANCE

Soil microbes are responsible for critical biogeochemical processes in natural and agricultural ecosystems. Despite their importance, the functional traits of most soil organisms remain woefully under-characterized, limiting our ability to understand how microbial populations influence the transformation of elements such as nitrogen (N) in soil. Quantitative stable isotope probing (qSIP) is a powerful tool to measure the traits of individual taxa. This method has rarely been applied in the field or with 15N to measure nitrogen assimilation. In this study, we measured genus-specific microbial nitrogen assimilation in two agricultural soils and compared field and lab 15N qSIP methods. Our results identify taxa important for nitrogen assimilation in agricultural soils, shed light on the field relevance of lab qSIP studies, and provide guidance for the future application of qSIP to measure microbial traits in the field.

Variations in microbial community compositions and processes imposed under contrast geochemical contexts in Sicilian mud volcanoes, Italy

Terrestrial mud volcanoes represent surface features of channels for subsurface methane transport and, therefore, constitute an important source of methane emission from natural environments. How microbial processes regulate methane emissions in terrestrial mud volcanoes has yet to be fully addressed. This study demonstrated the geochemical characteristics and microbial communities of four mud volcano and seep sites in two geological settings of Sicily, Italy. At sites within the accretionary wedge that exhibited higher methane and sulfate concentrations, the communities were dominated by members capable of catalyzing methane and sulfate metabolisms and organic degradation. In particular, both anaerobic and aerobic methanotrophs were abundant and their abundance distribution coincided with the geochemical transition. In contrast, the sites near Mount Etna were characterized by high fluid salinity, CO2, and low methane and sulfate concentrations, with communities consisting of halophilic organic degraders and sulfur metabolizers, along with a minor presence of aerobic methanotrophs. Substantial variations in community composition and geochemistry across spatial and vertical redox gradients suggest that physicochemical contexts imposed by the geology, fluid path, and source characteristics play a vital role in shaping community composition and cycling of methane, sulfur and organic carbon in Sicily mud volcanoes.

Circular metagenome-assembled genome of Candidatus Cloacimonadota recovered from anaerobic digestion sludge

This study reports a circular metagenome-assembled genome (cMAG) of Candidatus Cloacimonadota recovered from a mesophilic full-scale food waste treatment plant. The cMAG spans 2,298,113 bp, with 980× coverage and 1 contig.

Organic matter degradation in the deep, sulfidic waters of the Black Sea: insights into the ecophysiology of novel anaerobic bacteria

BACKGROUND

Recent studies have reported the identity and functions of key anaerobes involved in the degradation of organic matter (OM) in deep (> 1000 m) sulfidic marine habitats. However, due to the lack of available isolates, detailed investigation of their physiology has been precluded. In this study, we cultivated and characterized the ecophysiology of a wide range of novel anaerobes potentially involved in OM degradation in deep (2000 m depth) sulfidic waters of the Black Sea.

RESULTS

We have successfully cultivated a diverse group of novel anaerobes belonging to various phyla, including Fusobacteriota (strain S5), Bacillota (strains A1T and A2), Spirochaetota (strains M1T, M2, and S2), Bacteroidota (strains B1T, B2, S6, L6, SYP, and M2P), Cloacimonadota (Cloa-SY6), Planctomycetota (Plnct-SY6), Mycoplasmatota (Izemo-BS), Chloroflexota (Chflx-SY6), and Desulfobacterota (strains S3T and S3-i). These microorganisms were able to grow at an elevated hydrostatic pressure of up to 50 MPa. Moreover, this study revealed that different anaerobes were specialized in degrading specific types of OM. Strains affiliated with the phyla Fusobacteriota, Bacillota, Planctomycetota, and Mycoplasmatota were found to be specialized in the degradation of cellulose, cellobiose, chitin, and DNA, respectively, while strains affiliated with Spirochaetota, Bacteroidota, Cloacimonadota, and Chloroflexota preferred to ferment less complex forms of OM. We also identified members of the phylum Desulfobacterota as terminal oxidizers, potentially involved in the consumption of hydrogen produced during fermentation. These results were supported by the identification of genes in the (meta)genomes of the cultivated microbial taxa which encode proteins of specific metabolic pathways. Additionally, we analyzed the composition of membrane lipids of selected taxa, which could be critical for their survival in the harsh environment of the deep sulfidic waters and could potentially be used as biosignatures for these strains in the sulfidic waters of the Black Sea.

CONCLUSIONS

This is the first report that demonstrates the cultivation and ecophysiology of such a diverse group of microorganisms from any sulfidic marine habitat. Collectively, this study provides a step forward in our understanding of the microbes thriving in the extreme conditions of the deep sulfidic waters of the Black Sea. Video Abstract.

Aragonite crystallization in a sulfate-rich hypersaline wetland under dry Mediterranean climate (Laguna Honda, eastern Guadalquivir basin, S Spain)

This research investigates the influence of water composition, the presence of seasonal algal mats, detrital inputs and the activity of microorganisms on the crystallization of aragonite in the sediments deposited in the hypersaline Laguna Honda wetland (S of Spain). The high alkaline and hypersaline waters (pH > 9.2 and C.E. > 70 mS/cm) of the wetland lake are rich in SO42- (>24,000 mg/l), Cl- (>21,000 mg/l), Na+ (>11,000 mg/l) Mg2+ (>8400 mg/l) and Ca2+ (>1000 mg/l), and are supersaturated for dolomite, calcite and aragonite. Sediments have lower pH values than column waters, oscillating from 8.54 in the low Eh (up to -80.9 mV) central deep sediments and 6.33 in the shallower higher Eh (around -13.6 mV) shore sediments. Erosion of the surrounding olive groves soils produced detrital silicates rich sediments with concretions of carbonate or sulfate. Aragonite (up to 19 %) and pyrite (up to 13 %) are mainly concentrated in the organic matter rich samples from the upper part of the sediment cores, whereas gypsum is preferably concentrated in low organic matter content samples. Mineral crusts containing a MgAl silicate phase, epsomite, halite and gypsum are precipitated on the floating algal mats covering the wetland waters. Floating algal mats deposit increased the organic matter content of the upper sediments which promoted the presence of fermentative microorganisms, sulfate-reducing bacteria (SRB) and sulfur-oxidizing bacteria (SOB) communities and variations of Eh that influence the authigenesis of carbonate and S-bearing minerals. Replacement of poorly crystalline MgSi phases infilling algal cells by aragonite was favored in the organic matter rich sediments with low Eh values and important SRB communities that promoted sulfate bioreduction processes to form pyrite. Aragonite precipitation was favored by the increase of carbonate and bicarbonate concentration produced by the SRB oxidation of organic matter, the CO2 degassing by high summer temperatures and the CO2 uptake by photosynthesis of the algal mats.

Uncultivated DPANN archaea are ubiquitous inhabitants of global oxygen-deficient zones with diverse metabolic potential

Archaea belonging to the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota) superphylum have been found in an expanding number of environments and perform a variety of biogeochemical roles, including contributing to carbon, sulfur, and nitrogen cycling. Generally characterized by ultrasmall cell sizes and reduced genomes, DPANN archaea may form mutualistic, commensal, or parasitic interactions with various archaeal and bacterial hosts, influencing the ecology and functioning of microbial communities. While DPANN archaea reportedly comprise a sizeable fraction of the archaeal community within marine oxygen-deficient zone (ODZ) water columns, little is known about their metabolic capabilities in these ecosystems. We report 33 novel metagenome-assembled genomes (MAGs) belonging to the DPANN phyla Nanoarchaeota, Pacearchaeota, Woesearchaeota, Undinarchaeota, Iainarchaeota, and SpSt-1190 from pelagic ODZs in the Eastern Tropical North Pacific and the Arabian Sea. We find these archaea to be permanent, stable residents of all three major ODZs only within anoxic depths, comprising up to 1% of the total microbial community and up to 25%-50% of archaea as estimated from read mapping to MAGs. ODZ DPANN appear to be capable of diverse metabolic functions, including fermentation, organic carbon scavenging, and the cycling of sulfur, hydrogen, and methane. Within a majority of ODZ DPANN, we identify a gene homologous to nitrous oxide reductase. Modeling analyses indicate the feasibility of a nitrous oxide reduction metabolism for host-attached symbionts, and the small genome sizes and reduced metabolic capabilities of most DPANN MAGs suggest host-associated lifestyles within ODZs.

IMPORTANCE

Archaea from the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota) superphylum have diverse metabolic capabilities and participate in multiple biogeochemical cycles. While metagenomics and enrichments have revealed that many DPANN are characterized by ultrasmall genomes, few biosynthetic genes, and episymbiotic lifestyles, much remains unknown about their biology. We report 33 new DPANN metagenome-assembled genomes originating from the three global marine oxygen-deficient zones (ODZs), the first from these regions. We survey DPANN abundance and distribution within the ODZ water column, investigate their biosynthetic capabilities, and report potential roles in the cycling of organic carbon, methane, and nitrogen. We test the hypothesis that nitrous oxide reductases found within several ODZ DPANN genomes may enable ultrasmall episymbionts to serve as nitrous oxide consumers when attached to a host nitrous oxide producer. Our results indicate DPANN archaea as ubiquitous residents within the anoxic core of ODZs with the potential to produce or consume key compounds.

Effects of environmental parameters on spatial and temporal distribution of marine microbial communities in the southern Black Sea

The Black Sea is a unique environment with strong and permanent vertical stratification, with a thin layer of oxic zone above and a permanent anoxic zone below. Few high-throughput genomic surveys have been conducted to examine microbiota in the Black Sea. Yet, there is no study on the seasonal and vertical variation in microbial community compositions, driving forces and mechanisms of community assembly. In this study, seasonal, vertical, and spatial microbial assemblages were studied in terms of diversity, abundance, and community structure using 16S rRNA metabarcoding. 16S rRNA metabarcoding confirmed seasonal changes in microbial communities and the presence of distinct microbial groups among different water layers. Taxa belonging to Cyanobiaceae contributed a large fraction of the total biomass and were the most abundant autotrophic bacteria found across the whole water column, including hydrogen sulfide-containing anoxic zone. Temperature, salinity, water density, conductivity, light, chlorophyll-a, O2, NO3, NH3, PO4, Si, and H2S had a significant influence on the vertical bacterial community assemblages. The copper mine discharge system at 180 m did not affect microbial community structure and composition. Temperature seemed to be a primary factor in the variance between shallow depths. In conclusion, the lack of light, low dissolved oxygen levels, and low temperature do not restrict microbial diversity, as proven by the higher diversity observed in deeper zones. Wastewater in Black Sea region may be discharged into the Black Sea to depth of 180 m or deeper without impacting microbial ecology.

Niche separation in bacterial communities and activities in porewater, loosely attached, and firmly attached fractions in permeable surface sediments

Heterotrophic microbes are central to organic matter degradation and transformation in marine sediments. Currently, most investigations of benthic microbiomes do not differentiate between processes in the porewater and on the grains and, hence, only show a generalized picture of the community. This limits our understanding of the structure and functions of sediment microbiomes. To address this problem, we fractionated sandy surface sediment microbial communities from a coastal site in Isfjorden, Svalbard, into cells associated with the porewater, loosely attached to grains, and firmly attached to grains; we found dissimilar bacterial communities and metabolic activities in these fractions. Most (84%-89%) of the cells were firmly attached, and this fraction comprised more anaerobes, such as sulfate reducers, than the other fractions. The porewater and loosely attached fractions (3% and 8%-13% of cells, respectively) had more aerobic heterotrophs. These two fractions generally showed a higher frequency of dividing cells, polysaccharide (laminarin) hydrolysis rates, and per-cell O2 consumption than the firmly attached cells. Thus, the different fractions occupy distinct niches within surface sediments: the firmly attached fraction is potentially made of cells colonizing areas on the grain that are protected from abrasion, but might be more diffusion-limited for organic matter and electron acceptors. In contrast, the porewater and loosely attached fractions are less resource-limited and have faster growth. Their cell numbers are kept low possibly through abrasion and exposure to grazers. Differences in community composition and activity of these cell fractions point to their distinct roles and contributions to carbon cycling within surface sediments.

Controls and significance of priming effects in lake sediments

Warming and eutrophication influence carbon (C) processing in sediments, with implications for the global greenhouse-gas budget. Temperature effects on sedimentary C loss are well understood, but the mechanism of change in turnover through priming with labile organic matter (OM) is not. Evaluating changes in the magnitude of priming as a function of warming, eutrophication, and OM stoichiometry, we incubated sediments with 13 C-labeled fresh organic matter (FOM, algal/cyanobacterial) and simulated future climate scenarios (+4°C and +8°C). We investigated FOM-induced production of CH4 and microbial community changes. C loss was primed by up to 17% in dominantly allochthonous sediments (ranging from 5% to 17%), compared to up to 6% in autochthonous sediments (-9% to 6%), suggesting that refractory OM is more susceptible to priming. The magnitude of priming was dependent on sediment OM stoichiometry (C/N ratio), the ratio of fresh labile OM to microbial biomass (FOM/MB), and temperature. Priming was strongest at 4°C when FOM/MB was below 50%. Addition of FOM was associated with activation and growth of bacterial decomposers, including for example, Firmicutes, Bacteroidetes, or Fibrobacteres, known for their potential to degrade insoluble and complex structural biopolymers. Using sedimentary C/N > 15 as a threshold, we show that in up to 35% of global lakes, sedimentation is dominated by allochthonous rather than autochthonous material. We then provide first-order estimates showing that, upon increase in phytoplankton biomass in these lakes, priming-enabled degradation of recalcitrant OM will release up to 2.1 Tg C annually, which would otherwise be buried for geological times.

Unraveling the interplay between antibiotic resistance genes and microbial communities in water and sediments of the intensive tidal flat aquaculture

Tidal flats are formed valuably resources by the interaction of terrestrial and marine processes. Aquaculture on tidal flats has brought significant economic profits, but the over usage of antibiotics has resulted in the prevalence antibiotic resistance genes (ARGs) which pose serious threats to ecosystems. However, ARG abundances and bacterial community assemblies in the overlying water and sediments of tidal flat aquaculture areas have not been fully explored. Thus, antibiotic concentrations, ARG abundances, microbial communities and the influences of environmental factors in the Jiangsu tidal flat aquaculture ponds were investigated using high-throughput sequencing and qPCR. The concentrations of antibiotics at sampling ranged from not detectable to 2322.4 ng g-1, and sulfamethazine and ciprofloxacin were the dominant antibiotics. The sul1 and sul2 abundances were highest and the ARG abundances were higher in sediment than in water. Meanwhile, bacterial community diversities and structures were significantly different (P < 0.05) between water and sediment samples. Network analysis identified Sphingomonadacear, Pseudomonas, and Xanthobacteraceae as potential ARG-carrying pathogens. A positive correlation between ARGs and intI1 indicated that horizontal gene transfer occurred in water, while antibiotics and TN significantly influenced ARG abundances in sediment. Neutral modeling showed that deterministic and stochastic processes contributed most to the bacterial community assemblies of water and sediment samples, respectively. This study comprehensively illustrates the prevalence of ARGs in intensive tidal flat aquaculture regions and provides an effective foundation for the management of antibiotics usage.

Enhanced lead phytoextraction and soil health restoration through exogenous supply of organic ligands: Geochemical modeling"

Phytoremediation of lead (Pb) contaminated soil is a green technology to reduce Pb exposure and root exudates-derived organic acids play a vital role in this treatment process. In this study, Pb hyperaccumulator Pelargonium hortorum was chosen to investigate root-induced organic acid secretions and their subsequent role in Pb phytoextraction. In the first step, root exudation of P. hortorum was investigated in hydroponic experiments (0.2X Hoagland solution) under control and Pb stress conditions. Possible chemical interactions between Pb and the observed root exudates were then analyzed using Visual MINTEQ modeling. In the next step, the effects of the exogenous application of organic acids on Pb phytoextraction and soil enzymatic activities were studied in a pot experimental setup. Results indicated significant exudation of malic acid > citric acid > oxalic acid > tartaric acid in root exudates of P. hortorum under 50 mg L-1 Pb. Visual MINTEQ modeling results revealed that organic acids directly affect Pb dissolution in the nutrient solution by modulation of solution pH. Experimental results revealed that malic acid and citric acid significantly increased available Pb contents (7.2- and 6.7-folds) in the soil with 1500 mg kg-1 Pb contamination. Whereas, in shoot and root, the highest increase in Pb concentration was observed with citric acid (2.01-fold) and malic (3.75-fold) supplements, respectively. Overall, Pb uptake was notably higher when malic acid was applied (2.8-fold) compared to other organic acids, followed by citric acid (2.7-fold). In the case of soil enzymatic activities, oxalic acid significantly improved dehydrogenase, alkaline phosphatase, and microbial biomass by 1.6-, 1.4- and 1.3-folds, respectively. The organic acids were successful in reviving enzyme activity in Pb-contaminated soil, and might thus be used for long-term soil regeneration.

Phylogenetically and metabolically diverse autotrophs in the world's deepest blue hole

The world's deepest yongle blue hole (YBH) is characterized by sharp dissolved oxygen (DO) gradients, and considerably low-organic-carbon and high-inorganic-carbon concentrations that may support active autotrophic communities. To understand metabolic strategies of autotrophic communities for obtaining carbon and energy spanning redox gradients, we presented finer characterizations of microbial community, metagenome and metagenome-assembled genomes (MAGs) in the YBH possessing oxic, hypoxic, essentially anoxic and completely anoxic zones vertically. Firstly, the YBH microbial composition and function shifted across the four zones, linking to different biogeochemical processes. The recovery of high-quality MAGs belonging to various uncultivated lineages reflected high novelty of the YBH microbiome. Secondly, carbon fixation processes and associated energy metabolisms varied with the vertical zones. The Calvin-Benson-Bassham (CBB) cycle was ubiquitous but differed in affiliated taxa at different zones. Various carbon fixation pathways were found in the hypoxic and essentially anoxic zones, including the 3-hyroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle affiliated to Nitrososphaeria, and Wood-Ljungdahl (WL) pathway affiliated to Planctomycetes, with sulfur oxidation and dissimilatory nitrate reduction as primary energy-conserving pathways. The completely anoxic zone harbored diverse taxa (Dehalococcoidales, Desulfobacterales and Desulfatiglandales) utilizing the WL pathway coupled with versatile energy-conserving pathways via sulfate reduction, fermentation, CO oxidation and hydrogen metabolism. Finally, most of the WL-pathway containing taxa displayed a mixotrophic lifestyle corresponding to flexible carbon acquisition strategies. Our result showed a vertical transition of microbial lifestyle from photo-autotrophy, chemoautotrophy to mixotrophy in the YBH, enabling a better understanding of carbon fixation processes and associated biogeochemical impacts with different oxygen availability.

Metagenomic 16S rDNA reads of in situ preserved samples revealed microbial communities in the Yongle blue hole

Our knowledge on biogeochemistry and microbial ecology of marine blue holes is limited due to challenges in collecting multilayered water column and oxycline zones. In this study, we collected samples from 16 water layers in Yongle blue hole (YBH) located in the South China Sea using the in situ microbial filtration and fixation (ISMIFF) apparatus. The microbial communities based on 16S rRNA metagenomic reads for the ISMIFF samples showed high microbial diversity and consistency among samples with similar dissolved oxygen levels. At the same depth of the anoxic layer, the ISMIFF samples were dominated by sulfate-reducing bacteria from Desulfatiglandales (17.96%). The sulfide concentration is the most significant factor that drives the division of microbial communities in YBH, which might support the prevalence of sulfate-reducing microorganisms in the anoxic layers. Our results are different from the microbial community structures of a Niskin sample of this study and the reported samples collected in 2017, in which a high relative abundance of Alteromonadales (26.59%) and Thiomicrospirales (38.13%), and Arcobacteraceae (11.74%) was identified. We therefore demonstrate a new profile of microbial communities in YBH probably due to the effect of sampling and molecular biological methods, which provides new possibilities for further understanding of the material circulation mechanism of blue holes and expanding anoxic marine water zones under global warming.

Uncultivated DPANN archaea are ubiquitous inhabitants of global oxygen deficient zones with diverse metabolic potential

Archaea belonging to the DPANN superphylum have been found within an expanding number of environments and perform a variety of biogeochemical roles, including contributing to carbon, sulfur, and nitrogen cycling. Generally characterized by ultrasmall cell sizes and reduced genomes, DPANN archaea may form mutualistic, commensal, or parasitic interactions with various archaeal and bacterial hosts, influencing the ecology and functioning of microbial communities. While DPANN archaea reportedly comprise 15-26% of the archaeal community within marine oxygen deficient zone (ODZ) water columns, little is known about their metabolic capabilities in these ecosystems. We report 33 novel metagenome-assembled genomes belonging to DPANN phyla Nanoarchaeota, Pacearchaeota, Woesarchaeota, Undinarchaeota, Iainarchaeota, and SpSt-1190 from pelagic ODZs in the Eastern Tropical North Pacific and Arabian Sea. We find these archaea to be permanent, stable residents of all 3 major ODZs only within anoxic depths, comprising up to 1% of the total microbial community and up to 25-50% of archaea. ODZ DPANN appear capable of diverse metabolic functions, including fermentation, organic carbon scavenging, and the cycling of sulfur, hydrogen, and methane. Within a majority of ODZ DPANN, we identify a gene homologous to nitrous oxide reductase. Modeling analyses indicate the feasibility of a nitrous oxide reduction metabolism for host-attached symbionts, and the small genome sizes and reduced metabolic capabilities of most DPANN MAGs suggest host-associated lifestyles within ODZs.

Bravo A, Heimburger Boavida LE. Redox gradient shapes the abundance and diversity of mercury-methylating microorganisms along the water column of the Black Sea

In the global context of seawater deoxygenation triggered by climate change and anthropogenic activities, changes in redox gradients impacting biogeochemical transformations of pollutants, such as mercury, become more likely. Being the largest anoxic basin worldwide, with high concentrations of the potent neurotoxic methylmercury (MeHg), the Black Sea is an ideal natural laboratory to provide new insights about the link between dissolved oxygen concentration and hgcAB gene-carrying (hgc+) microorganisms involved in the formation of MeHg. We combined geochemical and microbial approaches to assess the effect of vertical redox gradients on abundance, diversity, and metabolic potential of hgc+ microorganisms in the Black Sea water column. The abundance of hgcA genes [congruently estimated by quantitative PCR (qPCR) and metagenomics] correlated with MeHg concentration, both maximal in the upper part of the anoxic water. Besides the predominant Desulfobacterales, hgc+ microorganisms belonged to a unique assemblage of diverse-previously underappreciated-anaerobic fermenters from Anaerolineales, Phycisphaerae (characteristic of the anoxic and sulfidic zone), Kiritimatiellales, and Bacteroidales (characteristic of the suboxic zone). The metabolic versatility of Desulfobacterota differed from strict sulfate reduction in the anoxic water to reduction of various electron acceptors in the suboxic water. Linking microbial activity and contaminant concentration in environmental studies is rare due to the complexity of biological pathways. In this study, we disentangle the role of oxygen in shaping the distribution of Hg-methylating microorganisms consistently with MeHg concentration, and we highlight their taxonomic and metabolic niche partitioning across redox gradients, improving the prediction of the response of marine communities to the expansion of oxygen-deficient zones. IMPORTANCE Methylmercury (MeHg) is a neurotoxin detected at high concentrations in certain marine ecosystems, posing a threat to human health. MeHg production is mainly mediated by hgcAB gene-carrying (hgc+) microorganisms. Oxygen is one of the main factors controlling Hg methylation; however, its effect on the diversity and ecology of hgc+ microorganisms remains unknown. Under the current context of seawater deoxygenation, mercury cycling is expected to be disturbed. Here, we show the strong effect of oxygen gradients on the distribution of potential Hg methylators. In addition, we show for the first time the significant contribution of a unique assemblage of potential fermenters from Anaerolineales, Phycisphaerae, and Kiritimatiellales to Hg methylation, stratified in different redox niches along the Black Sea gradient. Our results considerably expand the known taxonomic diversity and ecological niches prone to the formation of MeHg and contribute to better apprehend the consequences of oxygen depletion in seawater.

Mediation of Bacterial Interactions via a Novel Membrane-Based Segregator to Enhance Biological Nitrogen Removal

The regulation of microbial subpopulations in wastewater treatment plants (WWTPs) with desired functions can guarantee nutrient removal. In nature, "good fences make good neighbors," which can be applied to engineering microbial consortia. Herein, a membrane-based segregator (MBSR) was proposed, where porous membranes not only promote the diffusion of metabolic products but also isolate incompatible microbes. The MBSR was integrated with an anoxic/aerobic membrane bioreactor (i.e., an experimental MBR). The long-term operation showed that the experimental MBR exhibited higher nitrogen removal (10.45 ± 2.73 mg/L total nitrogen) than the control MBR (21.68 ± 4.23 mg/L) in the effluent. The MBSR resulted in much lower oxygen reduction potential in the anoxic tank of the experimental MBR (-82.00 mV) compared to that of the control MBR (83.25 mV). The lower oxygen reduction potential can inevitably aid in the occurrence of denitrification. The 16S rRNA sequencing showed that the MBSR significantly enriched acidogenic consortia, which yielded considerable volatile fatty acids by fermenting the added carbon sources and allowed efficient transfer of these small molecules to the denitrifying community. Moreover, the sludge communities of the experimental MBR harbored a higher abundance of denitrifying bacteria than those of the control MBR. Metagenomic analysis further corroborated these sequencing results. The spatially structured microbial communities in the experimental MBR system demonstrate the practicability of the MBSR, achieving nitrogen removal efficiency superior to that of mixed populations. Our study provides an engineering method for modulating the assembly and metabolic division of labor of subpopulations in WWTPs. IMPORTANCE This study provides an innovative and applicable method for regulating subpopulations (activated sludge and acidogenic consortia), which contributes to the precise control of the metabolic division of labor in biological wastewater treatment processes.

Viruses of sulfur oxidizing phototrophs encode genes for pigment, carbon, and sulfur metabolisms

Viral infections modulate bacterial metabolism and ecology. Here, we investigated the hypothesis that viruses influence the ecology of purple and green sulfur bacteria in anoxic and sulfidic lakes, analogs of euxinic oceans in the geologic past. By screening metagenomes from lake sediments and water column, in addition to publicly-available genomes of cultured purple and green sulfur bacteria, we identified almost 300 high and medium-quality viral genomes. Viruses carrying the gene psbA, encoding the small subunit of photosystem II protein D1, were ubiquitous, suggesting viral interference with the light reactions of sulfur oxidizing autotrophs. Viruses predicted to infect these autotrophs also encoded auxiliary metabolic genes for reductive sulfur assimilation as cysteine, pigment production, and carbon fixation. These observations show that viruses have the genomic potential to modulate the production of metabolic markers of phototrophic sulfur bacteria that are used to identify photic zone euxinia in the geologic past.

Hyperactive nanobacteria with host-dependent traits pervade Omnitrophota

Candidate bacterial phylum Omnitrophota has not been isolated and is poorly understood. We analysed 72 newly sequenced and 349 existing Omnitrophota genomes representing 6 classes and 276 species, along with Earth Microbiome Project data to evaluate habitat, metabolic traits and lifestyles. We applied fluorescence-activated cell sorting and differential size filtration, and showed that most Omnitrophota are ultra-small (~0.2 μm) cells that are found in water, sediments and soils. Omnitrophota genomes in 6 classes are reduced, but maintain major biosynthetic and energy conservation pathways, including acetogenesis (with or without the Wood-Ljungdahl pathway) and diverse respirations. At least 64% of Omnitrophota genomes encode gene clusters typical of bacterial symbionts, suggesting host-associated lifestyles. We repurposed quantitative stable-isotope probing data from soils dominated by andesite, basalt or granite weathering and identified 3 families with high isotope uptake consistent with obligate bacterial predators. We propose that most Omnitrophota inhabit various ecosystems as predators or parasites.

Bioprospecting for Novel Bacterial Sources of Hydrolytic Enzymes and Antimicrobials in the Romanian Littoral Zone of the Black Sea

Marine microorganisms have evolved a large variety of metabolites and biochemical processes, providing great opportunities for biotechnologies. In the search for new hydrolytic enzymes and antimicrobial compounds with enhanced characteristics, the current study explored the diversity of cultured and uncultured marine bacteria in Black Sea water from two locations along the Romanian coastline. Microbial cell density in the investigated samples varied between 65 and 12.7 × 10³ CFU·mL^-1. The total bacterial community identified by Illumina sequencing of 16S rRNA gene comprised 185 genera belonging to 46 classes, mainly Gammaproteobacteria, Alphaproteobacteria, Flavobacteriia, and 24 phyla. The 66 bacterial strains isolated on seawater-based culture media belonged to 33 genera and showed variable growth temperatures, growth rates, and salt tolerance. A great fraction of these strains, including Pseudoalteromonas and Flavobacterium species, produced extracellular proteases, lipases, and carbohydrases, while two strains belonging to the genera Aquimarina and Streptomyces exhibited antimicrobial activity against human pathogenic bacteria. This study led to a broader view on the diversity of microbial communities in the Black Sea, and provided new marine strains with hydrolytic and antimicrobial capabilities that may be exploited in industrial and pharmaceutical applications.

Transient Oxygen Exposure Causes Profound and Lasting Changes to a Benzene-Degrading Methanogenic Community

We investigated the impact of oxygen on a strictly anaerobic, methanogenic benzene-degrading enrichment culture derived decades ago from oil-contaminated sediment. The culture includes a benzene fermenter from Deltaproteobacteria candidate clade Sva0485 (referred to as ORM2) and methanogenic archaea. A one-time injection of 0.1 mL air , simulating a small leak into 30 mL batch culture bottle, had no measurable impact on benzene degradation rates, although retrospectively, a tiny enrichment of aerobic taxa was detected. A subsequent 100 times larger injection of air stalled methanogenesis and caused drastic perturbation of the microbial community. A benzene-degrading Pseudomonas became highly enriched and consumed all available oxygen. Anaerobic benzene-degrading ORM2 cell numbers plummeted during this time; re-growth and associated recovery of methanogenic benzene degradation took almost 1 year. These results highlight the oxygen sensitivity of this methanogenic culture and confirm that the mechanism for anaerobic biotransformation of benzene is independent of oxygen, fundamentally different from established aerobic pathways, and is carried out by distinct microbial communities. The study also highlights the importance of including microbial decay in characterizing and modeling mixed microbial communities.

Overlying water fluoride concentrations influence dissolved organic matter composition and migration from pore water in sediment via bacterial mechanisms

Fluoride (F-) is widespread in aquatic environments; however, it is not clear whether the fluctuation of F- concentrations in overlying lake water affects the composition and migration of dissolved organic matter (DOM) from sediment. A case study was presented in Sand Lake, China, and an experiment was conducted to analyze the influence of different F- concentrations in overlying water on DOM characteristics. Diffusion resulted in similarities in DOM components between overlying and pore waters, and bacterial activities and enzyme variation resulted in differences between them. Higher F- concentrations in overlying water resulted in a higher pH of pore water, which favored the enrichment of protein-like substances. Higher F- concentrations caused lower DOM concentrations and lower maximum fluorescence intensities (Fmax) of protein-like components in pore water. The F- concentrations had significantly negative correlations with Shannon indexes (P < 0.05). Thiobacillus influenced the migration of tyrosine-like substances by decreasing the pH of pore water. Trichococcus and Fusibacter altered the Fmax of protein-like, humic-like, and fulvic-like substances. The F- concentrations affected the DOM composition and migration due to the response of functional bacterial communities, which were positively correlated with the relative abundance of Thiobacillus and negatively correlated with the relative abundances of Trichococcus and Fusibacter. The high F- concentrations influenced the biosynthesis and degradation of protein-like substances by shifting the abundances of the relevant enzymes. The results of this study may provide ideas for investigating DOM cycling under the influence of F-, especially in lakes with fluctuations in F- concentrations.

Signature of dissolved organic matter and microbial communities based on different oxygen levels response during distillers dried grains with solubles plus sugarcane pith co-fermentations

The objective of this study was to investigate the relationship between dissolved organic matter (DOM) and microbial communities during the co-fermentation of distillers dried grains with solubles (DDGS) and sugarcane pith at different oxygen levels. In aerobic fermentation (AF), the content of DOM decreased from 32.61 mg/g to 14.14 mg/g, and decreased from 32.61 mg/g to 30.83 mg/g in anaerobic fermentation (ANF). Phenols and alcohols were consumed first in AF, while lipids and proteins were consumed first in ANF. Degradation rates of cellulose, hemicellulose and lignin in AF (6.67%, 39.93%, 36.50%) were higher than those in ANF (0.69%, 18.36%, 9.12%). Firmicutes, Actinobacteriota and Ascomycota were the main phyla in community. Distance-based redundancy analysis showed that pH, organic matter (OM) and DOM were the main driving factors of microbial community succession.

The physiology and metabolic properties of a novel, low-abundance Psychrilyobacter species isolated from the anoxic Black Sea shed light on its ecological role

Members of the Psychrilyobacter spp. of the phylum Fusobacteria have been recently suggested to be amongst the most significant primary degraders of the detrital organic matter in sulfidic marine habitats, despite representing only a small proportion (<0.1%) of the microbial community. In this study, we have isolated a previously uncultured Psychrilyobacter species (strains SD5^T and BL5; Psychrilyobacter piezotolerans sp. nov.) from the sulfidic waters (i.e., 2000 m depth) of the Black Sea and investigated its physiology and genomic capability in order to better understand potential ecological adaptation strategies. P. piezotolerans utilized a broad range of organic substituents (carbohydrates and proteins) and, remarkably, grew at sulfide concentrations up to 32 mM. These flexible physiological properties were supported by the presence of the respective metabolic pathways in the genomes of both strains. Growth at varying hydrostatic pressure (0.1-50 MPa) was sustained by modifying its membrane lipid composition. Thus, we have isolated a novel member of the 'rare biosphere', which endures the extreme conditions and may play a significant role in the degradation of detrital organic matter sinking into the sulfidic waters of the Black Sea.

Shedding Light on Microbial "Dark Matter": Insights Into Novel Cloacimonadota and Omnitrophota From an Antarctic Lake

The potential metabolism and ecological roles of many microbial taxa remain unknown because insufficient genomic data are available to assess their functional potential. Two such microbial "dark matter" taxa are the Candidatus bacterial phyla Cloacimonadota and Omnitrophota, both of which have been identified in global anoxic environments, including (but not limited to) organic-carbon-rich lakes. Using 24 metagenome-assembled genomes (MAGs) obtained from an Antarctic lake (Ace Lake, Vestfold Hills), novel lineages and novel metabolic traits were identified for both phyla. The Cloacimonadota MAGs exhibited a capacity for carbon fixation using the reverse tricarboxylic acid cycle driven by oxidation of hydrogen and sulfur. Certain Cloacimonadota MAGs encoded proteins that possess dockerin and cohesin domains, which is consistent with the assembly of extracellular cellulosome-like structures that are used for degradation of polypeptides and polysaccharides. The Omnitrophota MAGs represented phylogenetically diverse taxa that were predicted to possess a strong biosynthetic capacity for amino acids, nucleosides, fatty acids, and essential cofactors. All of the Omnitrophota were inferred to be obligate fermentative heterotrophs that utilize a relatively narrow range of organic compounds, have an incomplete tricarboxylic acid cycle, and possess a single hydrogenase gene important for achieving redox balance in the cell. We reason that both Cloacimonadota and Omnitrophota form metabolic interactions with hydrogen-consuming partners (methanogens and Desulfobacterota, respectively) and, therefore, occupy specific niches in Ace Lake.

Microbial Roles in Dissolved Organic Matter Transformation in Full-Scale Wastewater Treatment Processes Revealed by Reactomics and Comparative Genomics

Understanding the degradation of dissolved organic matter (DOM) is vital for optimizing DOM control. However, the microbe-mediated DOM transformation during wastewater treatment remains poorly characterized. Here, microbes and DOM along full-scale biotreatment processes were simultaneously characterized using comparative genomics and high-resolution mass spectrometry-based reactomics. Biotreatments significantly increased DOM's aromaticity and unsaturation due to the overproduced lignin and polyphenol analogs. DOM was diversified by over five times in richness, with thousands of nitrogenous and sulfur-containing compounds generated through microbe-mediated oxidoreduction, functional group transfer, and C-N and C-S bond formation. Network analysis demonstrated microbial division of labor in DOM transformation. However, their roles were determined by their functional traits rather than taxa. Specifically, network and module hubs exhibited rapid growth potentials and broad substrate affinities but were deficient in xenobiotics-metabolism-associated genes. They were mainly correlated to liable DOM consumption and its transformation to recalcitrant compounds. In contrast, connectors and peripherals were potential degraders of recalcitrant DOM but slow in growth. They showed specialized associations with fewer DOM molecules and probably fed on metabolites of hub microbes. Thus, developing technologies (e.g., carriers) to selectively enrich peripheral degraders and consequently decouple the liable and recalcitrant DOM transformation processes may advance DOM removal.

Gulf of Mexico blue hole harbors high levels of novel microbial lineages

Exploration of oxygen-depleted marine environments has consistently revealed novel microbial taxa and metabolic capabilities that expand our understanding of microbial evolution and ecology. Marine blue holes are shallow karst formations characterized by low oxygen and high organic matter content. They are logistically challenging to sample, and thus our understanding of their biogeochemistry and microbial ecology is limited. We present a metagenomic and geochemical characterization of Amberjack Hole on the Florida continental shelf (Gulf of Mexico). Dissolved oxygen became depleted at the hole's rim (32 m water depth), remained low but detectable in an intermediate hypoxic zone (40-75 m), and then increased to a secondary peak before falling below detection in the bottom layer (80-110 m), concomitant with increases in nutrients, dissolved iron, and a series of sequentially more reduced sulfur species. Microbial communities in the bottom layer contained heretofore undocumented levels of the recently discovered phylum Woesearchaeota (up to 58% of the community), along with lineages in the bacterial Candidate Phyla Radiation (CPR). Thirty-one high-quality metagenome-assembled genomes (MAGs) showed extensive biochemical capabilities for sulfur and nitrogen cycling, as well as for resisting and respiring arsenic. One uncharacterized gene associated with a CPR lineage differentiated hypoxic from anoxic zone communities. Overall, microbial communities and geochemical profiles were stable across two sampling dates in the spring and fall of 2019. The blue hole habitat is a natural marine laboratory that provides opportunities for sampling taxa with under-characterized but potentially important roles in redox-stratified microbial processes.

Lipidomics of Environmental Microbial Communities. II: Characterization Using Molecular Networking and Information Theory

Structurally diverse, specialized lipids are crucial components of microbial membranes and other organelles and play essential roles in ecological functioning. The detection of such lipids in the environment can reveal not only the occurrence of specific microbes but also the physicochemical conditions to which they are adapted to. Traditionally, liquid chromatography coupled with mass spectrometry allowed for the detection of lipids based on chromatographic separation and individual peak identification, resulting in a limited data acquisition and targeting of certain lipid groups. Here, we explored a comprehensive profiling of microbial lipids throughout the water column of a marine euxinic basin (Black Sea) using ultra high-pressure liquid chromatography coupled with high-resolution tandem mass spectrometry (UHPLC-HRMS/MS). An information theory framework combined with molecular networking based on the similarity of the mass spectra of lipids enabled us to capture lipidomic diversity and specificity in the environment, identify novel lipids, differentiate microbial sources within a lipid group, and discover potential biomarkers for biogeochemical processes. The workflow presented here allows microbial ecologists and biogeochemists to process quickly and efficiently vast amounts of lipidome data to understand microbial lipids characteristics in ecosystems.

Niche partitioning of bacterial communities along the stratified water column in the Black Sea

The Black Sea is the largest semi‐closed permanently anoxic basin on our planet with long‐term stratification. The study aimed at describing the Black Sea microbial community taxonomic and functional composition within the range of depths spanning across oxic/anoxic interface, and to uncover the factors behind both their vertical and regional differentiation. 16S rRNA gene MiSeq sequencing was applied to get the data on microbial community taxonomy, and the PICRUSt pipeline was used to infer their functional profile. The normoxic zone was mainly inhabited by primary producers and heterotrophic prokaryotes (e.g., Flavobacteriaceae, Rhodobacteraceae, Synechococcaceae) whereas the euxinic zone—by heterotrophic and chemoautotrophic taxa (e.g., MSBL2, Piscirickettsiaceae, and Desulfarculaceae). Assimilatory sulfate reduction and oxygenic photosynthesis were prevailing within the normoxic zone, while the role of nitrification, dissimilatory sulfate reduction, and anoxygenic photosynthesis increased in the oxygen‐depleted water column part. Regional differentiation of microbial communities between the Ukrainian shelf and offshore zone was detected as well, yet it was significantly less pronounced than the vertical one. It is suggested that regional differentiation within a well‐oxygenated zone is driven by the difference in phytoplankton communities providing various substrates for the prokaryotes, whereas redox stratification is the main driving force behind microbial community vertical structure.

The bacterial sulfur cycle in expanding dysoxic and euxinic marine waters

Dysoxic marine waters (DMW, < 1 μM oxygen) are currently expanding in volume in the oceans, which has biogeochemical, ecological and societal consequences on a global scale. In these environments, distinct bacteria drive an active sulfur cycle, which has only recently been recognized for open-ocean DMW. This review summarizes the current knowledge on these sulfur-cycling bacteria. Critical bottlenecks and questions for future research are specifically addressed. Sulfate-reducing bacteria (SRB) are core members of DMW. However, their roles are not entirely clear, and they remain largely uncultured. We found support for their remarkable diversity and taxonomic novelty by mining metagenome-assembled genomes from the Black Sea as model ecosystem. We highlight recent insights into the metabolism of key sulfur-oxidizing SUP05 and Sulfurimonas bacteria, and discuss the probable involvement of uncultivated SAR324 and BS-GSO2 bacteria in sulfur oxidation. Uncultivated Marinimicrobia bacteria with a presumed organoheterotrophic metabolism are abundant in DMW. Like SRB, they may use specific molybdoenzymes to conserve energy from the oxidation, reduction or disproportionation of sulfur cycle intermediates such as S0 and thiosulfate, produced from the oxidation of sulfide. We expect that tailored sampling methods and a renewed focus on cultivation will yield deeper insight into sulfur-cycling bacteria in DMW.

Microbial community development on model particles in the deep sulfidic waters of the Black Sea

Microorganisms attached to particles have been shown to be different from free-living microbes and to display diverse metabolic activities. However, little is known about the ecotypes associated with particles and their substrate preference in anoxic marine waters. Here, we investigate the microbial community colonizing particles in the anoxic and sulfide-rich waters of the Black Sea. We incubated beads coated with different substrates in situ at 1000 and 2000 m depth. After 6 h, the particle-attached microbes were dominated by Gamma- and Alpha-proteobacteria, and groups related to the phyla Latescibacteria, Bacteroidetes, Planctomycetes and Firmicutes, with substantial variation across the bead types, indicating that the attaching communities were selected by the substrate. Further laboratory incubations for 7 days suggested the presence of a community of highly specialized taxa. After incubation for 35 days, the microbial composition across all beads and depths was similar and primarily composed of putative sulfur cycling microbes. In addition to the major shared microbial groups, subdominant taxa on chitin and protein-coated beads were detected pointing to specialized microbial degraders. These results highlight the role of particles as sites for attachment and biofilm formation, while the composition of organic matter defined a secondary part of the microbial community.

Sulfurization of dissolved organic matter in the anoxic water column of the Black Sea

Today's oceans store as much dissolved organic carbon (DOC) in the water column as there is CO₂ in the atmosphere, and as such dissolved organic matter (DOM) is an important component of the global carbon cycle. It was shown that in anoxic marine sediments, reduced sulfur species (e.g., H₂S) abiotically react with organic matter, contributing to carbon preservation. It is not known whether such processes also contribute to preserving DOM in ocean waters. Here, we show DOM sulfurization within the sulfidic waters of the Black Sea, by combining elemental, isotopic, and molecular analyses. Dissolved organic sulfur (DOS) is formed largely in the water column and not derived from sediments or allochthonous nonmarine sources. Our findings suggest that during large-scale anoxic events, DOM may accumulate through abiotic reactions with reduced sulfur species, having long-lasting effects on global climate by enhancing organic carbon sequestration.

Organic Matter Type Defines the Composition of Active Microbial Communities Originating From Anoxic Baltic Sea Sediments

Carbon cycling in anoxic marine sediments is dependent on uncultured microbial communities. Niches of heterotrophic microorganisms are defined by organic matter (OM) type and the different phases in OM degradation. We investigated how OM type defines microbial communities originating from organic-rich, anoxic sediments from the Baltic Sea. We compared changes in the sediment microbial community, after incubation with different stable isotope labeled OM types [i.e., particulate algal organic matter (PAOM), protein, and acetate], by using DNA stable isotope probing (DNA-SIP). Incorporation of 13C and/or 15N label was predominantly detected in members of the phyla Planctomycetes and Chloroflexi, which also formed the majority (>50%) of the original sediment community. While these phylum-level lineages incorporated label from all OM types, phylogenetic analyses revealed a niche separation at the order level. Members of the MSBL9 (Planctomycetes), the Anaerolineales (Chloroflexi), and the class Bathyarchaeota, were identified as initial degraders of carbohydrate-rich OM, while other uncultured orders, like the CCM11a and Phycisphaerales (Planctomycetes), Dehalococcoidia, and JG30-KF-CM66 (Chloroflexi), incorporated label also from protein and acetate. Our study highlights the importance of initial fermentation of complex carbon pools in shaping anoxic sediment microbial communities and reveals niche specialization at the order level for the most important initial degraders in anoxic sediments.

The microbiome of the Black Sea water column analyzed by shotgun and genome centric metagenomics

BACKGROUND

The Black Sea is the largest brackish water body in the world, although it is connected to the Mediterranean Sea and presents an upper water layer similar to some regions of the former, albeit with lower salinity and temperature. Despite its well-known hydrology and physicochemical features, this enormous water mass remains poorly studied at the microbial genomics level.

RESULTS

We have sampled its different water masses and analyzed the microbiome by shotgun and genome-resolved metagenomics, generating a large number of metagenome-assembled genomes (MAGs) from them. We found various similarities with previously described Black Sea metagenomic datasets, that show remarkable stability in its microbiome. Our datasets are also comparable to other marine anoxic water columns like the Cariaco Basin. The oxic zone resembles to standard marine (e.g. Mediterranean) photic zones, with Cyanobacteria (Synechococcus but a conspicuously absent Prochlorococcus), and photoheterotrophs domination (largely again with marine relatives). The chemocline presents very different characteristics from the oxic surface with many examples of chemolithotrophic metabolism (Thioglobus) and facultatively anaerobic microbes. The euxinic anaerobic zone presents, as expected, features in common with the bottom of meromictic lakes with a massive dominance of sulfate reduction as energy-generating metabolism, a few (but detectable) methanogenesis marker genes, and a large number of "dark matter" streamlined genomes of largely unpredictable ecology.

CONCLUSIONS

The Black Sea oxic zone presents many similarities to the global ocean while the redoxcline and euxinic water masses have similarities to other similar aquatic environments of marine (Cariaco Basin or other Black Sea regions) or freshwater (meromictic monimolimnion strata) origin. The MAG collection represents very well the different types of metabolisms expected in this kind of environment. We are adding critical information about this unique and important ecosystem and its microbiome.

Assessing the Effect of Humic Substances and Fe(III) as Potential Electron Acceptors for Anaerobic Methane Oxidation in a Marine Anoxic System

Marine anaerobic methane oxidation (AOM) is generally assumed to be coupled to sulfate reduction, via a consortium of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). ANME-1 are, however, often found as single cells, or only loosely aggregated with SRB, suggesting they perform a form of AOM independent of sulfate reduction. Oxidized metals and humic substances have been suggested as potential electron acceptors for ANME, but up to now, AOM linked to reduction of these compounds has only been shown for the ANME-2 and ANME-3 clades. Here, the effect of the electron acceptors anthraquinone-disulfonate (AQDS), a humic acids analog, and Fe3+ on anaerobic methane oxidation were assessed by incubation experiments with anoxic Black Sea water containing ANME-1b. Incubation experiments with 13C-methane and AQDS showed a stimulating effect of AQDS on methane oxidation. Fe3+ enhanced the ANME-1b abundance but did not substantially increase methane oxidation. Sodium molybdate, which was added as an inhibitor of sulfate reduction, surprisingly enhanced methane oxidation, possibly related to the dominant abundance of Sulfurospirillum in those incubations. The presented data suggest the potential involvement of ANME-1b in AQDS-enhanced anaerobic methane oxidation, possibly via electron shuttling to AQDS or via interaction with other members of the microbial community.

Microbial Processes and Microbial Communities in the Water Column of the Polar Meromictic Lake Bol'shie Khruslomeny at the White Sea Coast

Microbiological, molecular ecological, biogeochemical, and isotope geochemical research was carried out at the polar Lake Bol'shie Khruslomeny at the coast of the Kandalaksha Bay, White Sea in March and September 2017. The uppermost mixolimnion was oxic, with low salinity (3-5%). The lower chemocline layer was brown-green colored, with very high content of particulate organic matter (up to 11.8 mg C L-1). The lowermost monimolimnion had marine salinity (22-24%) and very high concentrations of sulfide (up to 18 mmol L-1) and CH4 (up to 1.8 mmol L-1). In the chemocline, total microbial abundance and the rate of anoxygenic photosynthesis were 8.8 × 106 cells mL-1 and 34.4 μmol C L-1 day-1, respectively. Both in March and September, sulfate reduction rate increased with depth, peaking (up to 0.6-1.1 μmol S L-1 day-1) in the lower chemocline. Methane oxidation rates in the chemocline were up to 85 and 180 nmol CH4 L-1 day-1 in March and September, respectively; stimulation of this process by light was observed in September. The percentages of cyanobacteria and methanotrophs in the layer where light-induced methane oxidation occurred were similar, ∼2.5% of the microbial community. Light did not stimulate methane oxidation in deeper layers. The carbon isotope composition of particulate organic matter (δ13C-Corg), dissolved carbonates (δ13C-DIC), and methane (δ13C- CH4) indicated high microbial activity in the chemocline. Analysis of the 16S rRNA gene sequences revealed predominance of Cyanobium cyanobacteria (order Synechococcales) in the mixolimnion. Green sulfur bacteria Chlorobium phaeovibrioides capable of anoxygenic photosynthesis constituted ∼20% of the chemocline community both in March and in September. Methyloprofundus gammaptoteobacteria (family Methylomonaceae) were present in the upper chemocline, where active methane oxidation occurred. During winter, cyanobacteria were less abundant in the chemocline, while methanotrophs occurred in higher horizons, including the under-ice layer. Chemolithotrophic gammaproteobacteria of the genus Thiomicrorhabdus, oxidizing reduced sulfur compounds at low oxygen concentrations, were revealed in the chemocline in March. Both in March and September archaea constituted up to 50% of all microorganisms in the hypolimnion. The percentage of putative methanogens in the archaeal community was low, and they occurred mainly in near-bottom horizons.

Physiological, chemotaxonomic and genomic characterization of two novel piezotolerant bacteria of the family Marinifilaceae isolated from sulfidic waters of the Black Sea

Diversity analyses of microbial enrichments obtained from deep sulfidic water (2000 m) collected from the Black Sea indicated the presence of eleven novel putative lineages of bacteria affiliated to the family Marinifilaceae of the phylum Bacteroidetes. Pure cultures were obtained for four strains (i.e. M1P^T, M3P, A4^T and 44) of this family, which could be grouped into two different clades based on their 16S rRNA gene sequences. All four strains were Gram-negative, rod-shaped and facultative anaerobic bacteria. The genomes of all strains were sequenced and physiological analyses were performed. All strains utilized a wide range of carbon sources, which was supported by the presence of the pathways involved in carbon utilization encoded by their genomes. The strains were able to grow at elevated hydrostatic pressure (up to 50 MPa), which coincided with increased production of unsaturated and branched fatty acids, and a decrease in hydroxy fatty acids. Intact polar lipid analysis of all four strains showed the production of ornithine lipids, phosphatidylethanolamines and capnine lipids as major intact polar lipids (IPLs). Genes involved in hopanoid biosynthesis were also identified. However, bacteriohopanepolyols (BHPs) were not detected in the strains. Based on distinct physiological, chemotaxonomic, genotypic and phylogenetic differences compared to other members of the genera Ancylomarina and Labilibaculum, it was concluded that strains M1P^T and A4^T represented two novel species for which the names Ancylomarina euxinus sp. nov. and Labilibaculum euxinus sp. nov., respectively, are proposed.